We had that issue with version 8 and I opened a ticket with BB (#582521). Gary Harper sorted the problem out. There was a grade centre component that stopped the delete. Eventually BB supplied some sql to remove the course.
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From: Blackboard/Courseinfo userslist [mailto:[log in to unmask]] On Behalf Of CLAY Gary M
Sent: 22 September 2011 10:00
To: [log in to unmask]
Subject: Courses that can't be deleted (release 8)
Hass anyone else come across a situation where when you try to delete a course site the system gets so far e.g. removes the users but leaves the site in place?
The only solution we've found is to delete the items, folders, etc one by one and thence the system will then delete the course so I'd be interested to learn from others with similar experience especially if they have identified a better solution?
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